readFITS {FITSio}R Documentation

Read a single data set from a FITS file

Description

Read a single image (multi-dimensional array) or binary table from a FITS file. The source code readFITS.r is a model for creating code to read more complex FITS files.

Usage

readFITS(file = "R.fits", hdu = 1, phdu = 1)

Arguments

file existing FITS file name.
hdu position of Header and Data Unit (HDU) in FITS file: 1 for the first HDU, 2 for the second HDU, etc.
phdu rarely needed; see Details.

Details

readFITS is a simple but complete FITS file reader, automatically detecting image and binary table data extensions (ASCII tables and random groups are not supported in this release). It reads a single Header and Data Unit (HDU) pair from a file and returns a list with data, header, and axis information. Files with more complicated structures or isolated header units can be read with an appropriate combination of readFITSheader, readFITSarray, and readFITSbintable. See the Example section for readFITSimage for a step-by-step example that includes file opening and closing.

phdu = 0 forces a read of a secondary HDU in a fairly pathalogical case (specifically: indicating a read of a secondary HDU by setting NAXISn = 0 for n > 1, but NAXIS != 0 and NAXIS1 != 0.) This does not seem to be forbidden by the FITS standard but would be unlikely coding.

Binary table bit, complex, and array descriptor data types are not implemented in this release due to a lack of examples for testing.

Value

Return values from readFITS are a list depending on the data type:

imDat Data array (image).
axDat Data frame with axis scaling and labels (image).
hdr Vector with parsed header (all).
col Data from each column (bintable).
colNames Vector of column names, TTYPEn FITS variable (bintable).
colUnits Vector of column units, TUNITn FITS variable (bintable).
TNULLn Vector of undefined value definitions, FITS variable (bintable).
TSCALn Vector of multipliers for scaling, FITS variable (bintable).
TZEROn Vector of zeros for scaling, FITS variable (bintable).
TDISPn Vector of format information, FITS variable (bintable).

Note

Graphical FITS viewers such as fv (http://heasarc.gsfc.nasa.gov/ftools/fv/) and SAOImage DS9 (http://hea-www.harvard.edu/RD/ds9/) have excellent facilities for displaying FITS data, headers, and file structure. Having one or more graphical viewers available will prove extremely useful for working with FITS files, even when the data are read into R for further processing. fv and SAOImage DS9 are in active devlopement with support for unix, Windows, and Mac OS-X operating systems, and are available at no cost.

See readFrameFromFITS to read a binary table directly into an R data frame.

Author(s)

Andrew Harris

References

Hanisch et al., Astron. Astrophys. 376, 359-380 (2001)

http://fits.gsfc.nasa.gov/

See Also

readFITSarray, readFITSbintable, readFITSheader, readFrameFromFITS, image, par

Examples

require("FITSio")

### Image example
## Make test image with axis information, write to disk
Z <- matrix(1:15, ncol = 3)
writeFITSim(Z, file = "test.fits", c1 = "Test FITS file",
            crpix = c(1,1), crvaln = c(10, 100), cdeltn = c(8, 2),
            ctypen = c("Distance", "Time"),
            cunitn = c("Furlongs", "Fortnights"))
## Read back in and display
X <-  readFITS("test.fits")
ax1 <- axVec(1, X$axDat)          # Make axis vector for image
ax2 <- axVec(2, X$axDat)
xlab <- X$axDat$ctype[1]          
ylab <- paste(X$axDat$ctype[2], " [", X$axDat$cunit[2], "]", sep = "")
image(ax1, ax2, X$imDat, xlab = xlab, ylab = ylab)
summary(X)
X$axDat                           # Display data frame with axis data
X$hdr[1:10]                       # Header sample
X$hdr[which(X$hdr=="BITPIX")+1]   # BITPIX value from header
unlink("test.fits")
## No axis scale markings
image(X$imDat, xlab = xlab, ylab = ylab, xaxt = "n", yaxt = "n")

### Binary table examples
## Bintable with one row and differently multi-dimensional columns
## Either download example file from
## <http://fits.gsfc.nasa.gov/fits_samples.html>
## and use
## Not run: filename <- "IUElwp25637mxlo.fits"
## or, for local example use
filename <- system.file("fitsExamples", "IUElwp25637mxlo.fits",
                        package = "FITSio")  

Y <- readFITS(filename)
## Look at contents 
summary(Y)
Y$colNames
summary(Y$col)
Y$hdr[which(Y$hdr=="BITPIX")+1]   # BITPIX value from header
plot(Y$col[[5]], ylab = "Value", main = Y$colNames[5], type = "l")

### Simple flat file example
filename <- system.file("fitsExamples", "2008_03_11_203150.fits",
                        package = "FITSio")  
Z <- readFITS(filename) 
summary(Z)
Z$colNames
summary(Z$col)
attach(Z)
xc <- which(colNames == "DMJD")
yc <- which(colNames == "TiltX")
xlab <- paste(colNames[xc], " [", colUnits[xc], "]", sep = "")
ylab <- paste(colNames[yc], " [", colUnits[yc], "]", sep = "")
plot(col[[xc]], col[[yc]], xlab = xlab, ylab = ylab, type = "l")
detach(Z)


[Package FITSio version 1.0-2 Index]